The little success of breeding approaches toward the improvement of salt tolerance in crop species is thought to be attributable to the quantitative nature of most, if not all the processes implicated. Hence, the identification of some of the quantitative trait loci (QTL) that contribute to natural variation in salt tolerance should be instrumental in eventually manipulating the perception of salinity and the corresponding responses. A good choice to reach this goal is the plant model system Arabidopsis, whose complete genome sequence is now available. Aiming to analyze natural variability in salt tolerance, we have compared the ability of 102 wild-type races (named ecotypes or accessions) of Arabidopsis to germinate on 250 mm NaCl, finding a wide range of variation among them. Accessions displaying extremely different responses to NaCl were intercrossed, and the phenotypes found in their F 2 progenies suggested that natural variation in NaCl tolerance during germination was under polygenic controls. Genetic distances calculated on the basis of variations in repeat number at 22 microsatellites, were analyzed in a group of either extremely salt-tolerant or extremely salt-sensitive accessions. We found that most but not all accessions with similar responses to NaCl are phylogenetically related. NaCl tolerance was also studied in 100 recombinant inbred lines derived from a cross between the Columbia-4 and Landsberg erecta accessions. We detected 11 QTL harboring naturally occurring alleles that contribute to natural variation in NaCl tolerance in Arabidopsis, six at the germination and five at the vegetative growth stages, respectively. At least five of these QTL are likely to represent loci not yet described by their relationship with salt stress.A major factor impairing worldwide agricultural productivity is salinity, which is believed to affect nearly one-fifth of the world's irrigated land and causes 10 7 irrigated hectares to be abandoned each year (Boyer, 1982;Szaboles, 1987; Flowers and Yeo, 1995;Nelson et al., 1999). To solve the problems caused by salinity in agricultural areas, some engineering-based approaches have been applied, such as increased irrigation with water of high quality or soil drainage. Because these expensive solutions are not always practical, the study of plant salt tolerance, with a view to identifying and eventually manipulating the genes involved in salt perception and responses, seems to be a more promising approach.Plant salt tolerance is a complex trait, which is considered by many authors to be polygenic and hence difficult to dissect and manipulate. The variety of adaptive mechanisms that plants have evolved to cope with salt stress (McCue and Hanson, 1990) makes it difficult to choose of a single trait as a target for manipulation aimed at significantly improving plant salt tolerance. This might explain the lack of success of breeding programs developed with the aim of obtaining crop varieties able to tolerate salt stress while remaining productive in salinized lands (Flowers ...